Analysis of interatomic Contacts of Structural Units in PDB entry:
3UPU


Contacts of Structural Units (CSU) are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332).
For CSU analysis of other PDB entry

This page provides analyses of contacts formed by:
For analysis of ligand-protein contacts, use: 3D structure can be seen in additional window with STING software for 3UPU entry

There are 3 chains in PDB entry 3UPU (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 MSE 1VAL 439
B
 MSE 1VAL 439
C
 MSE 1LYS 368
Residue contacts

1. List of contacts for up to 10 consecutive residues:
Chain ID from residue number to residue number


2. Detailed analyses of contacts for any single residue:
Residue number chain ID
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There are 45 helices in PDB entry 3UPU. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
7 23Right-handed alpha
Helix 2
2
A
37 52Right-handed alpha
Helix 3
3
A
63 75Right-handed alpha
Helix 4
4
A
81 86Right-handed alpha
Helix 5
5
A
116 120Right-handed 310
Helix 6
6
A
121 132Right-handed alpha
Helix 7
7
A
160 164Right-handed 310
Helix 8
8
A
181 192Right-handed alpha
Helix 9
9
A
214 226Right-handed alpha
Helix 10
10
A
241 257Right-handed alpha
Helix 11
11
A
345 365Right-handed alpha
Helix 12
12
A
374 382Right-handed alpha
Helix 13
13
A
396 399Right-handed 310
Helix 14
14
A
411 416Right-handed 310
Helix 15
15
A
417 431Right-handed alpha
Helix 16
16
B
7 23Right-handed alpha
Helix 17
17
B
37 52Right-handed alpha
Helix 18
18
B
63 75Right-handed alpha
Helix 19
19
B
81 85Right-handed alpha
Helix 20
20
B
116 120Right-handed 310
Helix 21
21
B
121 130Right-handed alpha
Helix 22
22
B
160 164Right-handed 310
Helix 23
23
B
181 192Right-handed alpha
Helix 24
24
B
214 226Right-handed alpha
Helix 25
25
B
241 257Right-handed alpha
Helix 26
26
B
345 365Right-handed alpha
Helix 27
27
B
374 382Right-handed alpha
Helix 28
28
B
396 399Right-handed 310
Helix 29
29
B
411 416Right-handed 310
Helix 30
30
B
417 431Right-handed alpha
Helix 31
31
C
7 23Right-handed alpha
Helix 32
32
C
37 51Right-handed alpha
Helix 33
33
C
63 74Right-handed alpha
Helix 34
34
C
81 86Right-handed alpha
Helix 35
35
C
117 120Right-handed 310
Helix 36
36
C
121 132Right-handed alpha
Helix 37
37
C
160 164Right-handed 310
Helix 38
38
C
181 192Right-handed alpha
Helix 39
39
C
214 226Right-handed alpha
Helix 40
40
C
241 257Right-handed alpha
Helix 41
41
C
345 365Right-handed alpha
Helix 42
42
C
373 382Right-handed alpha
Helix 43
43
C
396 399Right-handed 310
Helix 44
44
C
411 416Right-handed 310
Helix 45
45
C
417 431Right-handed alpha
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There are 15 sheets in PDB entry 3UPU. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O,

There are 6 strands in A sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
78 80first strand
Strand 2
A
57 61parallel
Strand 3
A
111 114parallel
Strand 4
A
137 142parallel
Strand 5
A
27 31parallel
Strand 6
A
168 172parallel
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There are 2 strands in B sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
87 91first strand
Strand 2
A
96 100anti-parallel
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There are 6 strands in C sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
199 201first strand
Strand 2
A
204 208anti-parallel
Strand 3
A
432 439parallel
Strand 4
A
403 409parallel
Strand 5
A
235 239parallel
Strand 6
A
392 394parallel
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There are 5 strands in D sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
337 342first strand
Strand 2
A
318 329anti-parallel
Strand 3
A
296 309anti-parallel
Strand 4
A
268 271anti-parallel
Strand 5
A
387 389anti-parallel
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There are 2 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
275 281first strand
Strand 2
A
284 291anti-parallel
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There are 6 strands in F sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
79 80first strand
Strand 2
B
58 61parallel
Strand 3
B
111 114parallel
Strand 4
B
137 142parallel
Strand 5
B
27 31parallel
Strand 6
B
168 169parallel
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There are 2 strands in G sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
87 91first strand
Strand 2
B
96 100anti-parallel
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There are 6 strands in H sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
199 201first strand
Strand 2
B
204 208anti-parallel
Strand 3
B
432 439parallel
Strand 4
B
403 409parallel
Strand 5
B
235 239parallel
Strand 6
B
392 394parallel
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There are 6 strands in I sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
384 385first strand
Strand 2
B
337 342parallel
Strand 3
B
318 329anti-parallel
Strand 4
B
296 309anti-parallel
Strand 5
B
268 271anti-parallel
Strand 6
B
387 389anti-parallel
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There are 2 strands in J sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
275 281first strand
Strand 2
B
284 291anti-parallel
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There are 6 strands in K sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
78 80first strand
Strand 2
C
57 61parallel
Strand 3
C
111 115parallel
Strand 4
C
137 142parallel
Strand 5
C
27 31parallel
Strand 6
C
168 172parallel
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There are 2 strands in L sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
87 91first strand
Strand 2
C
96 100anti-parallel
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There are 6 strands in M sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
199 201first strand
Strand 2
C
204 208anti-parallel
Strand 3
C
432 439parallel
Strand 4
C
403 409parallel
Strand 5
C
235 239parallel
Strand 6
C
392 394parallel
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There are 6 strands in N sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
384 385first strand
Strand 2
C
337 342parallel
Strand 3
C
318 330anti-parallel
Strand 4
C
296 309anti-parallel
Strand 5
C
268 271anti-parallel
Strand 6
C
387 389anti-parallel
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There are 2 strands in O sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
275 281first strand
Strand 2
C
284 291anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il